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Started by upstream project "BIOFORMATS-test-repo" build number 237 originally caused by: Started by upstream project "Trigger" build number 262 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins4466973279804022847.sh + '[' cellsens = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_37305_merge_ci -v /uod/idr/repos/curated/cellsens:/data -v /uod/idr-scratch/merge-ci/curated/cellsens:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 02:51:37,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:51:37,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:51:37,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:51:37,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:51:37,469 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:51:37,469 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:51:37,469 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:51:37,469 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:51:37,470 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1139b2f3 - End of configuration. [testng] 02:51:37,470 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3f197a46 - Registering current configuration as safe fallback point [testng] 02:51:37,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@636be97c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 443 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-28 02:51:37,480] [main] java.version = 1.8.0_342 [testng] 02:51:37,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:51:37,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:37,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-28_02-51-37.log] [testng] 02:51:37,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-28 02:51:37,554] [main] testng.directory = /data [testng] [2024-10-28 02:51:37,555] [main] testng.configDirectory = /config [testng] [2024-10-28 02:51:37,599] [main] testng.multiplier = 1.0 [testng] [2024-10-28 02:51:37,600] [main] testng.in-memory = false [testng] [2024-10-28 02:51:37,600] [main] testng.allow-missing = false [testng] [2024-10-28 02:51:37,600] [main] user.language = fr [testng] [2024-10-28 02:51:37,600] [main] user.country = FR [testng] [2024-10-28 02:51:37,600] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-28 02:54:19,335] [main] ---------------------------------------- [testng] [2024-10-28 02:54:19,335] [main] Total files: 134 [testng] [2024-10-28 02:54:19,335] [main] Scan time: 161.735 s (1206 ms/file) [testng] [2024-10-28 02:54:19,335] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-28 02:55:07,571] [pool-1-thread-1] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] 02:55:07,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:55:07,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:07,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-28_02-55-07.log] [testng] 02:55:07,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d93c397 - End of configuration. [testng] [2024-10-28 02:55:07,841] [pool-1-thread-12] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] 02:55:07,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:55:07,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:07,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-28_02-55-07.log] [testng] 02:55:07,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53572b84 - End of configuration. [testng] [2024-10-28 02:55:08,478] [pool-1-thread-11] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] 02:55:08,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:55:08,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:08,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-28_02-55-08.log] [testng] 02:55:08,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@654d5b90 - End of configuration. [testng] [2024-10-28 02:55:08,753] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] 02:55:08,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:55:08,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:08,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-28_02-55-08.log] [testng] 02:55:08,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d5ebf9e - End of configuration. [testng] [2024-10-28 02:55:09,471] [pool-1-thread-9] Initializing /data/olivier/26-10-2014/Image_27_2.vsi: [testng] 02:55:09,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:55:09,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:09,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-28_02-55-09.log] [testng] 02:55:09,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d4f1ca - End of configuration. [testng] [2024-10-28 02:55:09,788] [pool-1-thread-8] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] 02:55:09,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:55:09,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:09,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-28_02-55-09.log] [testng] 02:55:09,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a263a35 - End of configuration. [testng] [2024-10-28 02:55:10,205] [pool-1-thread-7] Initializing /data/samples/Channels/svens cells - green.tif: [testng] 02:55:10,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:55:10,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:10,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-28_02-55-10.log] [testng] 02:55:10,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@113031cc - End of configuration. [testng] [2024-10-28 02:55:11,326] [pool-1-thread-6] Initializing /data/anthony/11R1398A1.vsi: [testng] 02:55:11,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:55:11,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:11,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-28_02-55-11.log] [testng] 02:55:11,328 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d773db9 - End of configuration. [testng] [2024-10-28 02:55:11,907] [pool-1-thread-5] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] 02:55:11,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:55:11,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:11,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-28_02-55-11.log] [testng] 02:55:11,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@731ddc30 - End of configuration. [testng] [2024-10-28 02:55:12,926] [pool-1-thread-4] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] 02:55:12,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:55:12,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:12,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-28_02-55-12.log] [testng] 02:55:12,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2711271e - End of configuration. [testng] [2024-10-28 02:55:13,228] [pool-1-thread-3] Initializing /data/olivier/Image_06.vsi: [testng] 02:55:13,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:55:13,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:13,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-28_02-55-13.log] [testng] 02:55:13,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@673ba7b9 - End of configuration. [testng] [2024-10-28 02:55:13,684] [pool-1-thread-2] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] 02:55:13,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:55:13,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:55:13,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-28_02-55-13.log] [testng] 02:55:13,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@dc9fe7c - End of configuration. [testng] [2024-10-28 02:55:19,729] [pool-1-thread-1] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-10-28 02:55:20,582] [pool-1-thread-2] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] [2024-10-28 02:55:21,278] [pool-1-thread-7] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] [2024-10-28 02:55:21,601] [pool-1-thread-12] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-10-28 02:55:22,065] [pool-1-thread-10] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] [2024-10-28 02:55:22,878] [pool-1-thread-5] Initializing /data/samples/Channels/Composite.vsi: [testng] [2024-10-28 02:55:26,022] [pool-1-thread-2] Initializing /data/robert/Lung_Mite.vsi: [testng] [2024-10-28 02:55:26,507] [pool-1-thread-5] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-10-28 02:55:28,153] [pool-1-thread-1] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-10-28 02:55:29,059] [pool-1-thread-10] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-10-28 02:55:32,217] [pool-1-thread-2] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-10-28 02:55:33,579] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-10-28 02:55:35,668] [pool-1-thread-1] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-10-28 02:55:36,687] [pool-1-thread-10] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-10-28 02:55:40,208] [pool-1-thread-5] Initializing /data/alex/test.vsi: [testng] [2024-10-28 02:55:41,631] [pool-1-thread-1] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] [2024-10-28 02:55:45,346] [pool-1-thread-5] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-10-28 02:55:48,514] [pool-1-thread-1] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-10-28 02:55:51,704] [pool-1-thread-5] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-10-28 02:56:05,380] [pool-1-thread-1] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-10-28 02:56:22,405] [pool-1-thread-3] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] [2024-10-28 02:56:29,488] [pool-1-thread-11] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-10-28 02:56:35,196] [pool-1-thread-11] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-10-28 02:57:12,142] [pool-1-thread-12] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] [2024-10-28 02:57:14,664] [pool-1-thread-12] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-10-28 02:57:19,082] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-10-28 02:57:26,702] [pool-1-thread-12] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-10-28 02:57:29,206] [pool-1-thread-10] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] [2024-10-28 02:57:35,120] [pool-1-thread-12] Initializing /data/gh-3822/image.jp2: [testng] [2024-10-28 02:57:46,001] [pool-1-thread-12] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-10-28 02:57:48,805] [pool-1-thread-5] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-10-28 02:57:55,733] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] [2024-10-28 02:58:01,268] [pool-1-thread-5] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] [2024-10-28 02:58:12,238] [pool-1-thread-9] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-10-28 02:58:12,916] [pool-1-thread-7] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-10-28 02:58:26,410] [pool-1-thread-10] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-10-28 02:58:30,788] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-10-28 02:58:35,422] [pool-1-thread-10] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-10-28 02:58:47,999] [pool-1-thread-2] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] [2024-10-28 02:58:52,613] [pool-1-thread-2] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-10-28 02:58:55,428] [pool-1-thread-7] Initializing /data/brian/Image_28.vsi: [testng] [2024-10-28 02:58:57,622] [pool-1-thread-2] Initializing /data/alex/pN1_new.vsi: [testng] [2024-10-28 02:59:03,923] [pool-1-thread-8] Initializing /data/qa-18870/Image_T30.vsi: [testng] [2024-10-28 02:59:04,716] [pool-1-thread-3] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] [2024-10-28 02:59:10,398] [pool-1-thread-3] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-10-28 02:59:28,084] [pool-1-thread-5] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] [2024-10-28 02:59:30,567] [pool-1-thread-5] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-10-28 02:59:41,359] [pool-1-thread-2] Initializing /data/brian/SW10082402-02_21.vsi: [testng] [2024-10-28 02:59:44,117] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] [2024-10-28 02:59:46,884] [pool-1-thread-12] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-10-28 02:59:49,422] [pool-1-thread-12] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-10-28 02:59:59,010] [pool-1-thread-4] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-10-28 03:00:02,041] [pool-1-thread-4] Initializing /data/qa-11039/Image_01.vsi: [testng] [2024-10-28 03:00:04,909] [pool-1-thread-12] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-10-28 03:00:08,870] [pool-1-thread-12] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-10-28 03:00:11,142] [pool-1-thread-12] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-10-28 03:00:15,167] [pool-1-thread-12] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] [2024-10-28 03:00:15,378] [pool-1-thread-7] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] [2024-10-28 03:00:19,701] [pool-1-thread-12] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-10-28 03:00:23,067] [pool-1-thread-12] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3816, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 38 seconds Finished: SUCCESS